Crystal Structure of Malonyl-CoA decarboxylase from Agrobacterium vitis, Northeast Structural Genomics Consortium Target RiR35

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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This is version 1.4 of the entry. See complete history


Crystal structures of malonyl-coenzyme a decarboxylase provide insights into its catalytic mechanism and disease-causing mutations.

Froese, D.S.Forouhar, F.Tran, T.H.Vollmar, M.Kim, Y.S.Lew, S.Neely, H.Seetharaman, J.Shen, Y.Xiao, R.Acton, T.B.Everett, J.K.Cannone, G.Puranik, S.Savitsky, P.Krojer, T.Pilka, E.S.Kiyani, W.Lee, W.H.Marsden, B.D.von Delft, F.Allerston, C.K.Spagnolo, L.Gileadi, O.Montelione, G.T.Oppermann, U.Yue, W.W.Tong, L.

(2013) Structure 21: 1182-1192

  • DOI: https://doi.org/10.1016/j.str.2013.05.001
  • Primary Citation of Related Structures:  
    2YGW, 4KS9, 4KSA, 4KSF

  • PubMed Abstract: 

    Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malonyl-CoA decarboxylase456Allorhizobium ampelinum S4Mutation(s): 0 
Gene Names: Avi_5372MCD (Avi_5372)
Find proteins for B9K0V9 (Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4))
Explore B9K0V9 
Go to UniProtKB:  B9K0V9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9K0V9
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.412α = 90
b = 100.412β = 90
c = 242.736γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection